How to Cut Costs on Shipping to Amazon Warehouses – 2025 Update

Shipping products to Amazon FBA warehouses is a major expense for third-party sellers. Whether you’re shipping a single box via SPD (Small Parcel Delivery) or pallet loads through LTL/FTL (Less Than Truckload/Full Truckload), shipping costs can eat up 15% to 40% of your total margin if not carefully optimized.

In 2025, with higher fuel surcharges, regional delivery bottlenecks, and Amazon’s stricter FBA receiving policies, cutting shipping costs is no longer optional—it’s a necessity for profitability.

Checklist for Cutting Amazon FBA Shipping Costs

1. Choose the Right Shipping Method: SPD vs. LTL/FTL

Many sellers default to SPD because it’s familiar and easier to set up. But as your shipment volume grows, this method quickly becomes inefficient. If you’re sending multiple boxes regularly, switching to LTL or FTL can significantly lower your per-unit cost.

LTL is ideal for 1–4 pallets, while FTL becomes more economical once you’re shipping 20+ pallets. The larger and more frequent your shipments, the more you save through freight consolidation and pallet optimization.

Always run a side-by-side cost analysis between Amazon’s partnered LTL and SPD options for the same shipment. Even at lower volumes, LTL can beat SPD in cost-per-unit when handled correctly.

2. Optimize Box and Pallet Dimensions

Smartly stacked boxes and pallets in Amazon warehouses highlight how optimizing dimensions helps maximize space utilization

Dimensional weight pricing has become the standard for carriers, meaning your shipping bill depends as much on volume as on actual weight. Oversized packaging, under-filled boxes, or poorly stacked pallets all translate into wasted money.

Even minor changes to your box dimensions can cut down on shipping charges significantly. It’s especially important to standardize carton sizes across SKUs and ensure you’re getting the most efficient stackability when using LTL or FTL.

A Freightos shipping case study found that by trimming box height by just 2 inches across 300 monthly units, one seller saved $420 in dimensional weight charges over 30 days.

3. Consolidate Shipments Strategically

Frequent small shipments often result in higher per-unit shipping costs, more carrier pickups, and a higher likelihood of fulfillment center delays. Consolidating multiple small shipments into a single, well-organized load saves on handling and often qualifies for better freight rates.

More importantly, Amazon prefers well-labeled, bulk deliveries over fragmented ones, which can
delay check-ins during peak seasons.

If you’re using a prep center or 3PL, schedule shipments biweekly or monthly instead of weekly. Many centers will hold goods for a few extra days to help you consolidate at no added cost.

4. Use a Prep Center Near Amazon FCs

A prep center near Amazon warehouses ensures faster and more accurate processing of shipments ready for dispatch

Shipping across the country adds avoidable costs, especially if your inventory is already located closer to Amazon’s main fulfillment hubs, according to Dollan Prep Center. Working with a prep center within a short distance of Amazon’s major FCs helps you reduce last-mile freight charges, shorten delivery windows, and reduce potential delays during appointment scheduling.

This also increases the chances of faster check-ins and fewer rescheduling penalties.

Relocating your prep and storage from the West Coast to Kentucky or Ohio can reduce per-pallet shipping costs by 20–30%, especially for sellers distributing nationwide.

5. Leverage Amazon’s Partnered Carrier Program

Amazon offers discounted rates through its partnered carrier program, which includes both UPS for SPD shipments and several freight providers for LTL and FTL loads. These discounts are only available if you create shipments directly through Seller Central and use Amazon’s pre-approved carriers.

In most cases, Amazon’s partnered rates beat outside quotes, even those from negotiated commercial accounts.

While you must comply with Amazon’s strict packaging and labeling requirements to access these rates, the savings are substantial, l—especially for high-volume sellers or those regularly shipping to distant FCs.

6. Reduce Rejected Shipments with Better Labeling and Packing

Neatly stacked boxes in Amazon warehouses demonstrate strategies to reduce rejected shipments and improve delivery efficiency

FBA rejections are costly and often entirely avoidable. If your shipment arrives with incorrect labels, mixed SKUs, damaged boxes, or non-standard pallets, Amazon may either reject the shipment or charge you additional fees for correction.

These mistakes lead to delays, inventory miscounts, and wasted freight costs. Proper prep practices—including double-checking barcode placements and securely packing all cartons—go a long way in avoiding financial hits.

Based on Amazon seller reports, approximately 1 in 5 shipments that result in receiving delays are traced back to labeling or prep errors, ot transport problems.

7. Compare 3PL and Freight Forwarder Rates

Freight pricing varies widely depending on your route, volume, and carrier network. Many sellers overlook potential savings by sticking with default options like Amazon Partnered LTL when they could secure lower rates via third-party logistics (3PL) providers or freight brokers.

For international shipments, especially from Asia, consider FBA-friendly freight forwarders who understand Amazon labeling and delivery protocols.

Always confirm that your 3PL or freight broker can handle Amazon’s strict delivery appointments and ASN documentation. Mishandled deliveries can delay check-in by days or even weeks.

8. Use Software to Automate and Optimize Shipping

Managing logistics manually might work at a small scale, but as your operation grows, automation is critical. FBA-compatible software can help you generate labels, track freight costs, schedule restocks, and reduce prep errors.

Most tools also offer data dashboards that allow you to compare historical shipping costs and identify which products are the most expensive to move.

Automating shipment creation and integrating freight cost visibility into your inventory management can help reduce administrative time by 20–30% and prevent avoidable prep center errors.

9. Negotiate Better Terms with Your Prep or Freight Providers

Shipping costs are not always fixed. If you’re consistently sending volume to FBA, you have leverage. Many prep centers, LTL brokers, and freight forwarders offer volume discounts, flat fees per pallet, or reduced storage costs if you ask.

Review your past 3–6 months of shipping data, calculate your average pallet count, and initiate a negotiation with your vendors.

Tip: Sellers averaging 10+ pallets per month can often secure flat monthly pallet rates, discounted receiving, or free shrink-wrapping—terms that reduce your cost per unit long term.

10. Eliminate Dead Weight: Audit Unprofitable Shipments

A focus on eliminating dead weight in Amazon warehouses leads to lighter, more cost-effective shipments

Not every product is worth shipping. It’s easy to fall into the trap of sending every piece of inventory to FBA, regardless of sales velocity or margin. Always review your SKU profitability before creating a shipment.

If a product yields less than $5 net profit after shipping and FBA fees, it may not be worth warehousing, especially if it ties up cash flow or increases long-term storage fees.

Sellers who regularly audit their shipping loads and purge underperforming inventory can reduce overall FBA shipping costs by 15–25%, according to Helium 10 seller data from Q4 2024.

Conclusion

Shipping costs are one of the easiest areas to improve once you understand the variables that impact pricing, from carton sizes to shipping method selection, from software automation to vendor negotiation.

In 2025, sellers who optimize these components can see thousands in annual savings and increase their margins without selling a single extra unit. Whether you’re operating at 500 units per month or 50,000, controlling your logistics pipeline will separate your business from competitors who let costs run unchecked.